Predicting protein secondary structure by an ensemble through feature-based accuracy estimation. - Spencer Krieger; John D. Kececioglu (BCB, 2020)

Boosting the accuracy of protein secondary structure prediction through nearest neighbor search and method hybridization. - Spencer Krieger; John D. Kececioglu (Bioinform., 2020)

Fast Approximate Shortest Hyperpaths for Inferring Pathways in Cell Signaling Hypergraphs. - Spencer Krieger; John D. Kececioglu (WABI, 2021)

Heuristic shortest hyperpaths in cell signaling hypergraphs. - Spencer Krieger; John D. Kececioglu (Algorithms Mol. Biol., 2022)

Correction: Heuristic shortest hyperpaths in cell signaling hypergraphs. - Spencer Krieger; John D. Kececioglu (Algorithms Mol. Biol., 2022)

Computing optimal factories in metabolic networks with negative regulation. - Spencer Krieger; John D. Kececioglu (Bioinform., 2022)

Computing Shortest Hyperpaths for Pathway Inference in Cellular Reaction Networks. - Spencer Krieger; John D. Kececioglu (RECOMB, 2023)

Shortest Hyperpaths in Directed Hypergraphs for Reaction Pathway Inference. - Spencer Krieger; John D. Kececioglu (J. Comput. Biol., 2023)

Computing Robust Optimal Factories in Metabolic Reaction Networks. - Spencer Krieger; John D. Kececioglu (RECOMB, 2024)

Robust Optimal Metabolic Factories. - Spencer Krieger; John D. Kececioglu (J. Comput. Biol., 2024)

Unified Integration of Spatial Transcriptomics Across Platforms. - Ellie Haber; Ajinkya Deshpande; Jian Ma 004; Spencer Krieger (RECOMB, 2025)